Comparative genomics is a powerful tool for uncovering patterns of mutations within genes targeted in human health concerns. To examine structure and function, we sequence targeted genes across multiple species to identify the pattern and rate of substitutions. This report summarizes our completion of projects, current ongoing research, and initiation of new advances with bioinformatic tools used to investigate gene function. In FY 2008-2009, we developed better methods to evaluate the over 4 Megabases (MB) of DNA sequence generated by LGD researchers for mammalian sex chromosomes in the cat family Felidae. This year, we add additional 2 (MB) of data for sex chromosomes in the Primate Order. Primate taxonomy is not easily resolved and has undergone considerable revision. The first suborder, Strepsirhini contains families Lemuridae (lemurs: now subdivided into familes of extant species Cheirogaleidae, and Lemuridae ), Indriidae (avahis, sifakas), Daubentoniidae (aye-ayes), and Lorisidae (lorises, pottos, and bushbabies). The second, Haplorhini, is composed of the families Cebidae (New World monkeys;some have partitioned into 5 families of Cebidae, Aotidae, Callicebidae, Pitheciidae, and Atelidae), Callithrichidae (marmosets and tamarins), Cercopithecidae (Old World Monkeys), Pongidae (gibbons: now in own family of Hylobatidae, and great apes), Tarsidae (tarsiers) and Hominidae (humans). Conflicting accounts of higher order relationships are common in the literature and change over time. Most of these studies are based on morphology and behavior, with some additional insights gleaned from molecular data. Our research will help to understand human origins and human evolution. Our ongoing initiative is the development and implementation of multiple bioinformatic methods to efficiently identify genes, map their position on mammalian X and Y-chromosomes of species other than human, and provide a context to interpret evolutionary processes leading that may have led to human diseases. We anticipate new insights through the recent incorporation of our whole genome studies of alpaca (artiodactyls), cat and pangolin (carnivore), and our ongoing phylogenetic investigation of over 200 species of primates. Additional tools are being developed to help annotate newly published and released primate Y chromosome sequence.